ID   NEP1_PYRCJ              Reviewed;         221 AA.
AC   A3MWJ1;
DT   15-JAN-2008, integrated into UniProtKB/Swiss-Prot.
DT   03-APR-2007, sequence version 1.
DT   03-AUG-2022, entry version 73.
DE   RecName: Full=Ribosomal RNA small subunit methyltransferase Nep1 {ECO:0000255|HAMAP-Rule:MF_00554};
DE            EC=2.1.1.- {ECO:0000255|HAMAP-Rule:MF_00554};
DE   AltName: Full=16S rRNA (pseudouridine-N1-)-methyltransferase Nep1 {ECO:0000255|HAMAP-Rule:MF_00554};
GN   Name=nep1 {ECO:0000255|HAMAP-Rule:MF_00554}; OrderedLocusNames=Pcal_1590;
OS   Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1).
OC   Archaea; Crenarchaeota; Thermoprotei; Thermoproteales; Thermoproteaceae;
OC   Pyrobaculum.
OX   NCBI_TaxID=410359;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=DSM 21063 / JCM 11548 / VA1;
RG   US DOE Joint Genome Institute;
RA   Copeland A., Lucas S., Lapidus A., Barry K., Glavina del Rio T., Dalin E.,
RA   Tice H., Pitluck S., Chain P., Malfatti S., Shin M., Vergez L., Schmutz J.,
RA   Larimer F., Land M., Hauser L., Kyrpides N., Mikhailova N., Cozen A.E.,
RA   Fitz-Gibbon S.T., House C.H., Saltikov C., Lowe T.M., Richardson P.;
RT   "Complete sequence of Pyrobaculum calidifontis JCM 11548.";
RL   Submitted (FEB-2007) to the EMBL/GenBank/DDBJ databases.
CC   -!- FUNCTION: Methyltransferase involved in ribosomal biogenesis.
CC       Specifically catalyzes the N1-methylation of the pseudouridine
CC       corresponding to position 914 in M.jannaschii 16S rRNA.
CC       {ECO:0000255|HAMAP-Rule:MF_00554}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=a pseudouridine in 16S/18S rRNA + S-adenosyl-L-methionine = an
CC         N(1)-methylpseudouridine in 16S/18S rRNA + H(+) + S-adenosyl-L-
CC         homocysteine; Xref=Rhea:RHEA:46696, Rhea:RHEA-COMP:11633, Rhea:RHEA-
CC         COMP:11634, ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC         ChEBI:CHEBI:65314, ChEBI:CHEBI:74890; Evidence={ECO:0000255|HAMAP-
CC         Rule:MF_00554};
CC   -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_00554}.
CC   -!- SIMILARITY: Belongs to the class IV-like SAM-binding methyltransferase
CC       superfamily. RNA methyltransferase NEP1 family. {ECO:0000305}.
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DR   EMBL; CP000561; ABO09008.1; -; Genomic_DNA.
DR   AlphaFoldDB; A3MWJ1; -.
DR   SMR; A3MWJ1; -.
DR   STRING; 410359.Pcal_1590; -.
DR   EnsemblBacteria; ABO09008; ABO09008; Pcal_1590.
DR   KEGG; pcl:Pcal_1590; -.
DR   eggNOG; arCOG04122; Archaea.
DR   HOGENOM; CLU_055846_1_3_2; -.
DR   OMA; VYVHTRN; -.
DR   Proteomes; UP000001431; Chromosome.
DR   GO; GO:0070037; F:rRNA (pseudouridine) methyltransferase activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0019843; F:rRNA binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0070475; P:rRNA base methylation; IEA:InterPro.
DR   CDD; cd18088; Nep1-like; 1.
DR   Gene3D; 3.40.1280.10; -; 1.
DR   HAMAP; MF_00554; NEP1; 1.
DR   InterPro; IPR029028; Alpha/beta_knot_MTases.
DR   InterPro; IPR005304; Rbsml_bgen_MeTrfase_EMG1/NEP1.
DR   InterPro; IPR023503; Ribosome_NEP1_arc.
DR   InterPro; IPR029026; tRNA_m1G_MTases_N.
DR   PANTHER; PTHR12636; PTHR12636; 1.
DR   Pfam; PF03587; EMG1; 1.
DR   SUPFAM; SSF75217; SSF75217; 1.
PE   3: Inferred from homology;
KW   Methyltransferase; Ribosome biogenesis; RNA-binding; rRNA processing;
KW   rRNA-binding; S-adenosyl-L-methionine; Transferase.
FT   CHAIN           1..221
FT                   /note="Ribosomal RNA small subunit methyltransferase Nep1"
FT                   /id="PRO_1000017929"
FT   BINDING         174
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00554"
FT   BINDING         179
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00554"
FT   BINDING         196..201
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00554"
FT   SITE            59
FT                   /note="Interaction with substrate rRNA"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00554"
FT   SITE            61
FT                   /note="Stabilizes Arg-59"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00554"
FT   SITE            100
FT                   /note="Interaction with substrate rRNA"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00554"
FT   SITE            103
FT                   /note="Interaction with substrate rRNA"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00554"
FT   SITE            107
FT                   /note="Interaction with substrate rRNA"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00554"
SQ   SEQUENCE   221 AA;  24080 MW;  90D917CF7BC8DC3D CRC64;
     MILVLAEAAL ELVPESLWRH PAIVADARRR GKKPGEILLD RARHHVAMAK LDKAERRGRP
     DIVHQVLLAF QYSLLNRAGR GRAFVHTVGD YIISVKPETR VPKNYNNFVS LMEQLFKVGR
     VPPEGEALME ARRGSLAALL EELGGKWVAL HEQGRAVSFA ELGRAVADAV VVVGGFPHGD
     FENKWILEGA EAVYKIGNVS LDAAQAVCRA VAAAEAALGL I